OptiDiff: structural variation detection from single optical mapping reads

Akdel, M.; de Ridder, D.

doi:10.1101/2022.01.08.475501

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bioRxiv · 10.1101/2022.01.08.475501

OptiDiff: structural variation detection from single optical mapping reads

Akdel, M.·de Ridder, D.

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Abstract

Detecting structural variation (SV) in eukaryotic genomes is of broad interest due to its often dramatic phenotypic effects, but remains a major, costly challenge based on DNA sequencing data. A cost-effective alternative in detecting large-scale SV has become available with advances in optical mapping technology. However, the algorithmic approaches to identifying SVs from optical mapping data are limited. Here, we propose a novel, open-source SV detection tool, OptiDiff, which employs a single molecule based approach to detect and classify homozygous and heterozygous SVs at coverages as low as 20x, showing better performance than the state of the art.

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Akdel, M., de Ridder, D.. 2022-01-11. OptiDiff: structural variation detection from single optical mapping reads. https://doi.org/10.1101/2022.01.08.475501

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